LAMMPS (8 Feb 2023)
# QMMM with PySCF - mixture example

units           real
atom_style      full

pair_style      lj/cut/coul/long 12
pair_modify     mix arithmetic

bond_style      harmonic
angle_style     harmonic
dihedral_style  none
improper_style  none

kspace_style    pppm 1e-5

read_data       data.mixture
Reading data file ...
  orthogonal box = (0 0 0) to (31.351877 31.351877 31.351877)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  3081 atoms
  reading velocities ...
  3081 velocities
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  reading bonds ...
  2055 bonds
  reading angles ...
  1033 angles
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     3 = max # of 1-3 neighbors
     3 = max # of 1-4 neighbors
     4 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.015 seconds

# QM atoms are IDs 1 to 9
# MM atoms are remaining atoms

group           qm id 1:9
9 atoms in group qm
group           mm subtract all qm
3072 atoms in group mm

# remove bonds/angles between QM atoms
# set charges to zero on QM atoms

delete_bonds    qm multi remove special
System init for delete_bonds ...
PPPM initialization ...
  using 12-bit tables for long-range coulomb (../kspace.cpp:342)
  G vector (1/distance) = 0.25751777
  grid = 24 24 24
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0020473396
  estimated relative force accuracy = 6.1655023e-06
  using double precision KISS FFT
  3d grid and FFT values/proc = 29791 13824
Generated 21 of 21 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 5 5 5
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Deleting bonds ...
  2048 total bonds, 2048 turned on, 0 turned off
  1024 total angles, 1024 turned on, 0 turned off
  0 total dihedrals, 0 turned on, 0 turned off
  0 total impropers, 0 turned on, 0 turned off
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     2 = max # of 1-2 neighbors
     1 = max # of 1-3 neighbors
     1 = max # of 1-4 neighbors
     4 = max # of special neighbors
  special bonds CPU = 0.000 seconds
set             group qm charge 0.0
Setting atom values ...
  9 settings made for charge

neighbor        2.0 bin
neigh_modify    delay 0 every 1 check yes

# QMMM dynamics

timestep        0.01

fix		1 all nve

fix             2 qm mdi/qmmm direct elements N H C H Cl O H
fix_modify      2 energy yes

thermo_style    custom step cpu temp ke evdwl ecoul epair emol elong                 f_2 pe etotal press

thermo          1

mdi             plugin pyscf_mdi mdi "-role ENGINE -name PySCF -method LINK"                 extra "-pbc no" command "run 2"
run 2
PPPM initialization ...
  using 12-bit tables for long-range coulomb (../kspace.cpp:342)
  G vector (1/distance) = 0.25751777
  grid = 24 24 24
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0020473396
  estimated relative force accuracy = 6.1655023e-06
  using double precision KISS FFT
  3d grid and FFT values/proc = 29791 13824
Generated 21 of 21 mixed pair_coeff terms from arithmetic mixing rule
Per MPI rank memory allocation (min/avg/max) = 26.88 | 26.88 | 26.88 Mbytes
   Step          CPU            Temp          KinEng         E_vdwl         E_coul         E_pair         E_mol          E_long          f_2           PotEng         TotEng         Press     
         0   0              0              0              103310.44      35284.412      88790.313      863.33521     -49804.536     -349295.05     -259641.4      -259641.4       897319.08    
         1   13.124098      631.94375      5801.8092      97293.123      35284.413      82773          863.33444     -49804.536     -349294.57     -265658.24     -259856.43      852336.04    
         2   27.177573      2211.4634      20303.213      82388.368      35284.413      67868.246      863.33213     -49804.536     -349292.7      -280561.12     -260257.91      741101.53    
Loop time of 27.1776 on 1 procs for 2 steps with 3081 atoms

Performance: 0.000 ns/day, 377466.604 hours/ns, 0.074 timesteps/s, 226.731 atom-step/s
96.6% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.040104   | 0.040104   | 0.040104   |   0.0 |  0.15
Bond    | 0.00012029 | 0.00012029 | 0.00012029 |   0.0 |  0.00
Kspace  | 0.003515   | 0.003515   | 0.003515   |   0.0 |  0.01
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00015099 | 0.00015099 | 0.00015099 |   0.0 |  0.00
Output  | 6.5629e-05 | 6.5629e-05 | 6.5629e-05 |   0.0 |  0.00
Modify  | 27.134     | 27.134     | 27.134     |   0.0 | 99.84
Other   |            | 9.209e-05  |            |       |  0.00

Nlocal:           3081 ave        3081 max        3081 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          17741 ave       17741 max       17741 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    1.77144e+06 ave 1.77144e+06 max 1.77144e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1771437
Ave neighs/atom = 574.95521
Ave special neighs/atom = 1.9941577
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:43
